Magic can accept "space" (nothing under the transistor) as equivalent to the substrate, under an nFET device. You can draw "pwell" or "psub" under an nFET if you want, but it doesn't have any particular significance (unless it's inside of a deep nwell structure). Either way, the bulk terminal will be connected into the global substrate node. If you want substrate areas to be semi-isolated nodes, you can put the "isosub" layer under them. Full R-C extraction does not yet know how to deal with multiple substrate regions, and I'm not sure how good its representation of networks across either substrate or nwells is.